CV

Education

• Graduate School of Chinese Academy of Agricultural Sciences, Agricultural Genomics Institution at Shen Zheng(2020-2023)
  • Graduate student
  • Major: Animal Husbandry
• Xidian University(2016-2020)
  • Undergraduate student
  • Major: Biotechnology

Current possition

• Spring 2024: Academic Pages Collaborator
  • Agricultural Genomics Institution at Shen Zheng, Graduate School of Chinese Academy of Agricultural Sciences.
  • Duties includes: Research assistant(Bioinformatcis)
  • Lab: Liu Yuwen lab

Skills

• Familiar with some machine learning models such as Transformer, ResNet, CNN, RNN and also classic cluster menthones like k-means, c-means.
• Basic statistics knowledge such as hypothesis testing and parameter estimation.
• Familiar with single cell RNA-seq and ATAC-seq data and also relevant software (cellranger and STARsolo), R (Seurat and ArchR) and python (Scanpy and Signac) packages.
• Proficient in Python and R scripts and machine learning packages (Pytorch and skite-learn).
• Familiar with linux system bash scripts.
• Familiar with multi-omices data (RNA-seq, ATAC-seq, CHIP-seq, WGS and etc) and bioinformatics common used software (BLAST, Bowtie, seqkit, samtools, bedtools,MEME and etc)

PROJECTS

Development of cross-species single-cell RNA-seq cell type annotation tool(CellLingo)

• Project design;
• Collected and analyzed single cell RNA-seq data from different species.
• Developed and trained heterogeneous graph convolutional neural network.

Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Porcine intestine during different developmental stages

• Quality controlled, Mapped and clustered cells.
• Integrated and analyzed scRNA-seq data and scATAC-seq data.
• Helped annotate cell types and analyzed cell-cell communication and RNA velocity.
• Visualized parts of result.

SKMATLAS: An integrated functional genomics database for vertebrate skeletal muscle

• Collected, filtered and analyzed parts of data.
• Designed website layout and functional tools on website.
• Wrote usage document for the website.
• The website can be explored by this URL: http://www.skmatlas.cn/

Prediction of potential animal reservoirs for the SARS-CoV-2 based on machine learning

• Collected data including all coronavirus’ spike protein sequence and their reservoirs hosts.
• Developed and trained a BPNN model.
• The result was similar to other researches about finding SARS-CoV-2 origins.

Patent

• Xian hui, Chen Ruipu et al. Machine learning-based analysis of the strength of the effect ofpromoters upstream of genes on expression:CN111613270A[P].2020-09-01.

Honors

• Gold Award in The 4th China International College Students’ “Internet+” Innovation and Entrepreneurship Competition (school level).
• The third place in The national finals of the 4th “i Creator” Science and Technology Innovation and Entrepreneurship Plan Competition.